I'm new here so this is my first post.I've been working on these engines for quite a few years and one trick that was taught to me by an older gentleman who was actually working as a Ford mechanic when these engine were first introduced was to trial fit the distributor when you first place the intake on the block.It is a little tricky with the cast iron intakes (heavy!) but the aluminum ones are a little easier. You can still move the intake around just a little before you cinch down the bolts.At that time the distributor should fall in place.You need to be careful but it does work.I always did this before putting any gaskets or sealer on.Once you have the exact location you can scribe marks in several places so you can line everything back up like you did in the trail fit up. I don't know if this is the problem you are running into but it has happened to me in the past.